Merge branch 'ModelingGenerator' of https://github.com/MyersResearchGroup/iBioSim into ModelingGenerator
This commit is contained in:
Pedro Fontanarrosa
commit
13a41a726e
20 changed files with 587 additions and 77 deletions
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@ -104,6 +104,7 @@ import javax.xml.xpath.XPathExpressionException;
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import org.antlr.runtime.ANTLRFileStream;
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import org.antlr.runtime.CommonTokenStream;
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import org.antlr.runtime.TokenStream;
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import org.apache.http.impl.client.HttpClients;
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import org.jdom2.JDOMException;
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import org.jlibsedml.AbstractTask;
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import org.jlibsedml.ArchiveComponents;
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@ -175,7 +176,6 @@ import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
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import edu.utah.ece.async.sboldesigner.sbol.editor.SynBioHubFrontends;
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import edu.utah.ece.async.sboldesigner.sbol.editor.dialog.RegistryInputDialog;
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import uk.ac.ebi.biomodels.ws.BioModelsWSClient;
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import uk.ac.ebi.biomodels.ws.BioModelsWSException;
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import de.unirostock.sems.cbarchive.ArchiveEntry;
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import de.unirostock.sems.cbarchive.CombineArchive;
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import de.unirostock.sems.cbarchive.CombineArchiveException;
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@ -200,6 +200,7 @@ import edu.utah.ece.async.ibiosim.dataModels.util.Message;
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import edu.utah.ece.async.ibiosim.dataModels.util.SEDMLutilities;
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import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
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import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObserver;
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import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.*;
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import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
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import edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisView;
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import edu.utah.ece.async.ibiosim.gui.graphEditor.Graph;
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@ -306,13 +307,11 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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protected String viewer;
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protected boolean runGetNames;
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// protected boolean showParts = false;
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// protected Thread getPartsThread = null;
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private String[] BioModelIds = null;
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private ModelSummary[] BioModelIds = null;
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// protected Parts allVirtualParts = null;
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@ -2758,20 +2757,44 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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}
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}
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private ModelSummary[] retrieveCuratedBioModels() {
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try(BioModelsConnectionService service = new BioModelsConnectionService()) {
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CuratedModelsResponse response = service.getCuratedModelSet();
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Set<ModelSummary> summaries = response.getModels();
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return summaries.toArray(new ModelSummary[summaries.size()]);
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}
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}
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private String getBioModelsModelFile(String modelId) {
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try(BioModelsConnectionService service = new BioModelsConnectionService()) {
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ModelFileResponse response = service.getModelFile(modelId);
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return response.getFileContent();
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}
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}
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private String getPublicationLinkForModel(String modelId) {
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try (BioModelsConnectionService service = new BioModelsConnectionService()) {
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ModelResponse modelInformation = service.getModel(modelId);
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if (null == modelInformation) {
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System.err.println("No entry found in BioModels for " + modelId);
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return null;
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}
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return modelInformation.getPublicationLink();
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}
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}
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private void downloadBioModel() {
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final BioModelsWSClient client = new BioModelsWSClient();
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if (BioModelIds == null) {
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try {
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BioModelIds = client.getAllCuratedModelsId();
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} catch (BioModelsWSException e2) {
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JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
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BioModelIds = retrieveCuratedBioModels();
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} catch (Exception e2) {
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JOptionPane.showMessageDialog(frame, "Error Contacting BioModels", "Error",
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JOptionPane.ERROR_MESSAGE);
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return;
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}
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}
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final JPanel BioModelsPanel = new JPanel(new BorderLayout());
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final JList ListOfBioModels = new JList();
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edu.utah.ece.async.ibiosim.dataModels.biomodel.util.Utility.sort(BioModelIds);
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final JList<ModelSummary> ListOfBioModels = new JList<>();
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ListOfBioModels.setListData(BioModelIds);
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ListOfBioModels.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
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JLabel TextBioModels = new JLabel("List of BioModels");
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@ -2780,65 +2803,28 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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ScrollBioModels.setPreferredSize(new Dimension(552, 250));
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ScrollBioModels.setViewportView(ListOfBioModels);
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JPanel GetButtons = new JPanel();
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JButton GetNames = new JButton("Get Names");
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JButton GetDescription = new JButton("Get Description");
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JButton GetReference = new JButton("Get Reference");
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final JProgressBar progressBar = new JProgressBar(0, 100);
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progressBar.setStringPainted(true);
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progressBar.setValue(0);
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runGetNames = true;
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final Thread getNamesThread = new Thread(new Runnable() {
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@Override
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public void run() {
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Preferences biosimrc = Preferences.userRoot();
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for (int i = 0; i < BioModelIds.length && runGetNames; i++) {
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try {
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progressBar.setValue(100 * i / BioModelIds.length);
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if (!BioModelIds[i].contains(" ")) {
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if (!biosimrc.get(BioModelIds[i], "").equals("")) {
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BioModelIds[i] += " " + biosimrc.get(BioModelIds[i], "");
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} else {
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String name = client.getModelNameById(BioModelIds[i]);
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biosimrc.put(BioModelIds[i], name);
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BioModelIds[i] += " " + name;
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}
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ListOfBioModels.setListData(BioModelIds);
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ListOfBioModels.revalidate();
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ListOfBioModels.repaint();
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}
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} catch (BioModelsWSException e1) {
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JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
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JOptionPane.ERROR_MESSAGE);
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runGetNames = false;
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}
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}
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progressBar.setValue(100);
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ListOfBioModels.setListData(BioModelIds);
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runGetNames = false;
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}
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});
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GetNames.addActionListener(new ActionListener() {
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@Override
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public void actionPerformed(ActionEvent e) {
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if (runGetNames && !getNamesThread.isAlive()) {
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getNamesThread.start();
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}
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}
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});
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GetDescription.addActionListener(new ActionListener() {
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@Override
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public void actionPerformed(ActionEvent e) {
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if (ListOfBioModels.isSelectionEmpty()) {
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return;
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}
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String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
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String selectedModel = ListOfBioModels.getSelectedValue().getId();
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Preferences biosimrc = Preferences.userRoot();
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String command = biosimrc.get("biosim.general.browser", "");
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command = command + " http://www.ebi.ac.uk/compneur-srv/biomodels-main/" + SelectedModel;
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command = command + " http://identifiers.org/biomodels.db/" + selectedModel;
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progressBar.setValue(25);
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log.addText("Executing:\n" + command + "\n");
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Runtime exec = Runtime.getRuntime();
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try {
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exec.exec(command);
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progressBar.setValue(100);
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} catch (IOException e1) {
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JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error",
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JOptionPane.ERROR_MESSAGE);
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@ -2851,25 +2837,31 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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if (ListOfBioModels.isSelectionEmpty()) {
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return;
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}
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String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
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ModelSummary model = ListOfBioModels.getSelectedValue();
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String modelId = model.getId();
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try {
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String Pub = (client.getSimpleModelById(SelectedModel)).getPublicationId();
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String pub = getPublicationLinkForModel(modelId);
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progressBar.setValue(25);
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progressBar.repaint();
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if (null == pub) {
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JOptionPane.showMessageDialog(frame,
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"Could not find publication information in BioModels for " + modelId,
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"Warning", JOptionPane.WARNING_MESSAGE);
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return;
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}
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Preferences biosimrc = Preferences.userRoot();
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String command = biosimrc.get("biosim.general.browser", "");
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command = command + " http://www.ncbi.nlm.nih.gov/pubmed/?term=" + Pub;
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command = command + ' ' + pub;
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log.addText("Executing:\n" + command + "\n");
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Runtime exec = Runtime.getRuntime();
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exec.exec(command);
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} catch (BioModelsWSException e2) {
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JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
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JOptionPane.ERROR_MESSAGE);
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progressBar.setValue(100);
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} catch (IOException e1) {
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JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error",
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JOptionPane.ERROR_MESSAGE);
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}
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}
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});
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GetButtons.add(GetNames);
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GetButtons.add(GetDescription);
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GetButtons.add(GetReference);
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GetButtons.add(progressBar);
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@ -2879,17 +2871,16 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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Object[] options = { "OK", "Cancel" };
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int value = JOptionPane.showOptionDialog(frame, BioModelsPanel, "List of BioModels", JOptionPane.YES_NO_OPTION,
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JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
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runGetNames = false;
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if (value == JOptionPane.YES_OPTION && ListOfBioModels.getSelectedValue() != null) {
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String ModelId = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
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String filename = ModelId + ".xml";
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String modelId = ListOfBioModels.getSelectedValue().getId();
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String filename = modelId + ".xml";
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try {
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if (overwrite(root + File.separator + filename, filename)) {
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String model = client.getModelSBMLById(ModelId);
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Writer out = new BufferedWriter(new OutputStreamWriter(
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new FileOutputStream(root + File.separator + filename), "UTF-8"));
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out.write(model);
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out.close();
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String model = getBioModelsModelFile(modelId);
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try (Writer out = new BufferedWriter(new OutputStreamWriter(
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new FileOutputStream(root + File.separator + filename), "UTF-8"))) {
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out.write(model);
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}
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String[] file = GlobalConstants.splitPath(filename.trim());
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SBMLDocument document = SBMLutilities.readSBML(root + File.separator + filename.trim(), null, this);
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Utils.check(root + File.separator + filename.trim(), document, false, null, this);
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@ -6147,7 +6138,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
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try
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{
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ComponentDefinition cd = getSBOLDocument().createComponentDefinition(partId, "1",
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ComponentDefinition.DNA);
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ComponentDefinition.DNA_REGION);
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cd.addRole(SequenceOntology.ENGINEERED_REGION);
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writeSBOLDocument();
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Set<ComponentDefinition> selectedDesign = new HashSet<ComponentDefinition>();
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@ -304,11 +304,11 @@ public class SBOLField2 extends JPanel implements ActionListener {
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*/
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private String getSpeciesSBOTerm(URI sbolSBOTerm)
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{
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if(sbolSBOTerm.equals(ComponentDefinition.DNA))
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if(sbolSBOTerm.equals(ComponentDefinition.DNA_REGION))
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{
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return GlobalConstants.SBO_DNA_SEGMENT;
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}
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else if(sbolSBOTerm.equals(ComponentDefinition.RNA))
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else if(sbolSBOTerm.equals(ComponentDefinition.RNA_REGION))
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{
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return GlobalConstants.SBO_RNA_SEGMENT;
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}
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